WikiSysop at 15:55, 7 September 2009

2009-09-07T15:55:18Z

WikiSysop: category

2009-09-07T13:08:44Z

WikiSysop: moved Phaser-2.2: XML to XML: take of phaser-2.2 page header so that it can be reused

2009-09-07T13:02:46Z

moved Phaser-2.2: XML to XML: take of phaser-2.2 page header so that it can be reused

WikiSysop: Protected "Phaser-2.2: XML" ([edit=sysop] (indefinite) [move=sysop] (indefinite))

2009-07-09T09:33:48Z

Protected "Phaser-2.2: XML" ([edit=sysop] (indefinite) [move=sysop] (indefinite))

WikiSysop: Initialization from almanac

2009-06-30T12:52:37Z

Initialization from almanac

New page

<div style="margin-left: 25px; float: right;">__TOC__</div>
Phaser can generate XML output from keyword input. XML output should be used in preference to grepping logfiles when incorporating Phaser into automation pipelines. Note that Phaser's python scripting ability is a more powerful way of calling Phaser for automation pipelines.

We would like to hear from developers who wish to incorporate Phaser into automation scripts using the XML functionality cimr-phaser@lists.cam.ac.uk

==How to Use XML Output==
===Generating XML Output===

Phaser outputs an XML file when called with the command line argument -xml followed by the filename for output.
<pre>
phaser -xml <filename>
</pre>
If no filename is given, Phaser exits immediately and writes an XML file with filename PHASER.XML describing the error (type="FILE OPENING", message="No XML filename").

===Tags===

All XML output is wrapped between "phaser" tags with the version number for the Phaser executable and the operating system on which the output was produced as attributes.
<pre>
<phaser version="2.1" ostype="linux">
---All Phaser XML output---
<\phaser>
</pre>
Names of files are output using the "file" tags with attributes "type" specifying reflections ("HKL") or coordinates ("XYZ") and attribute "format". Currently only "MTZ" and "PDB" formats are output.
<pre>
<file type="HKL" format="MTZ">filename</file>
<file type="XYZ" format="PDB">filename</file>
</pre>
Other XML tags are a combination of those suggested by the SPINE consortium and Phaser specific tags. There is no schema. Please refer to the examples.

===Error Handling===

Successful Phaser execution (not necessarily structure solution!) is reported as
<pre>
<status>ok</status>
</pre>
Failure during execution is reported as
<pre>
<status>error</status>
</pre>
More information about the type of error is given with
<pre>
<error>
<name>ERROR_NAME</name>
<message>ERROR_MESSAGE</message>
</error>
</pre>
Allowed values for ERROR_NAME are given in the table below, and specify the type of error. The ERROR_MESSAGE gives more information as to the specific cause of the error.
<pre>
ERROR_NAME Failure due to …
SYNTAX Syntax error in keyword input
INPUT Input error (e.g. invalid value for an input parameter)
FILE OPENING Unable to open file (given in ERROR_MESSAGE) for reading or writing.
OUT OF MEMORY Memory exhaustion
FATAL RUNTIME Fatal runtime error (e.g. bug in Phaser)
UNHANDLED Other unhandled fatal error (e.g. bug in libraries)
UNKNOWN Other error (e.g. bug in compiler)
</pre>

===Logfile Handling===

Use the keyword MUTE ON to prevent the writing of the logfile to standard output. Only the XML file and other results files (mtz,pdb) will be produced by Phaser.

==XML Output Examples==

Below are example XML output files produced by running the most popular modes of Phaser: anisotropy correction, automated molecular replacement, cell content analysis, normal mode analayis, and SAD phasing.

===Anisotropy Correction===

Output XML file for anisotropy correction of BETA-BLIP
<pre>
<phaser version="2.1" ostype="linux">
<status>ok</status>
<anisotropy_info>
<file type="HKL" format="MTZ">beta_blip_ano.mtz</file>
<eigenB type="1">10.88</eigenB>
<eigenB type="2">10.88</eigenB>
<eigenB type="3">-21.76</eigenB>
<eigenB type="delta">32.64</eigenB>
<wilson type="K">20.25</wilson>
<wilson type="B">56.97</wilson>
</anisotropy_info>
</phaser>
</pre>
===Cell Content Analysis===

Output XML file for Cell Content Analysis of BETA-BLIP
<pre>
<phaser version="2.1" ostype="linux">
<status>ok</status>
<cell_content_analysis_info>
<mw>46375.000000</mw>
<solution id="0"</cca>
<Z>1</Z>
<probVM>0.995130</probVM>
<VM>2.340743</VM>
</solution>
</cell_content_analysis_info>
</phaser>
</pre>

===Normal Mode Analysis===

Output XML file for Normal Mode Analysis of beta.pdb (modes 7 and 10, displacement forward only)
<pre>
<phaser version="2.1" ostype="linux">
<status>ok</status>
<normal_modes id="1">
<file type="XYZ" format="PDB">beta_nma.1.pdb</file>
<displacement mode="7">0.000000</displacement>
<displacement mode="10">0.000000</displacement>
</normal_modes>
<normal_modes id="2">
<file type="XYZ" format="PDB">beta_nma.2.pdb</file>
<displacement mode="7">0.000000</displacement>
<displacement mode="10">47.306646</displacement>
</normal_modes>
<normal_modes id="3">
<file type="XYZ" format="PDB">beta_nma.3.pdb</file>
<displacement mode="7">46.881456</displacement>
<displacement mode="10">0.000000</displacement>
</normal_modes>
<normal_modes id="4">
<file type="XYZ" format="PDB">beta_nma.4.pdb</file>
<displacement mode="7">46.881456</displacement>
<displacement mode="10">47.306646</displacement>
</normal_modes>
<normal_modes id="5">
<file type="XYZ" format="PDB">beta_nma.5.pdb</file>
<displacement mode="7">93.762912</displacement>
<displacement mode="10">0.000000</displacement>
</normal_modes>
<normal_modes id="6">
<file type="XYZ" format="PDB">beta_nma.6.pdb</file>
<displacement mode="7">93.762912</displacement>
<displacement mode="10">47.306646</displacement>
</normal_modes>
</phaser>
</pre>

===Automated Molecular Replacement===

Output XML file for Automated Molecular Replacement of BETA-BLIP
<pre>
<phaser version="2.1" ostype="linux">
<status>ok</status>
<dataset_info>
<cell>
<a>75.11</a>
<b>75.11</b>
<c>133.31</c>
<alpha>90</alpha>
<beta>90</beta>
<gamma>120</gamma>
</cell>
<spacegroup>
<hall> P 32 2"</hall>
<number>154</number>
<lattice>P</lattice>
<operator id="0">32</operator>
<operator id="1">2</operator>
<operator id="2">1</operator>
</spacegroup>
<n_symops>6</n_symops>
<symmetry_operator id="0">
<aa>1</aa> <ab>0</ab> <ac>0</ac> <atrans>0</atrans>
<ba>0</ba> <bb>1</bb> <bc>0</bc> <btrans>0</btrans>
<ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0</ctrans>
</symmetry_operator>
<symmetry_operator id="1">
<aa>0</aa> <ab>1</ab> <ac>0</ac> <atrans>0</atrans>
<ba>-1</ba> <bb>-1</bb> <bc>0</bc> <btrans>0</btrans>
<ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0.666667</ctrans>
</symmetry_operator>
<symmetry_operator id="2">
<aa>-1</aa> <ab>-1</ab> <ac>0</ac> <atrans>0</atrans>
<ba>1</ba> <bb>0</bb> <bc>0</bc> <btrans>0</btrans>
<ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0.333333</ctrans>
</symmetry_operator>
<symmetry_operator id="3">
<aa>0</aa> <ab>1</ab> <ac>0</ac> <atrans>0</atrans>
<ba>1</ba> <bb>0</bb> <bc>0</bc> <btrans>0</btrans>
<ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>0</ctrans>
</symmetry_operator>
<symmetry_operator id="4">
<aa>-1</aa> <ab>-1</ab> <ac>0</ac> <atrans>0</atrans>
<ba>0</ba> <bb>1</bb> <bc>0</bc> <btrans>0</btrans>
<ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>0.666667</ctrans>
</symmetry_operator>
<symmetry_operator id="5">
<aa>1</aa> <ab>0</ab> <ac>0</ac> <atrans>0</atrans>
<ba>-1</ba> <bb>-1</bb> <bc>0</bc> <btrans>0</btrans>
<ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>0.333333</ctrans>
</symmetry_operator>
</dataset_info>
<solution id="1">
<file type="HKL" format="MTZ">beta_blip.1.mtz</file>
<file type="XYZ" format="PDB">beta_blip.1.pdb</file>
<llg>996.141543</llg>
</solution>
</phaser>
</pre>

===Automated Experimental Phasing===
Output XML file for SAD phasing of insulin
<pre>
<phaser version="2.1" ostype="linux">
<status>ok</status>
<dataset_info>
<cell>
<a>78.046</a>
<b>78.046</b>
<c>78.046</c>
<alpha>90</alpha>
<beta>90</beta>
<gamma>90</gamma>
</cell>
<spacegroup>
<hall> I 2b 2c 3</hall>
<number>199</number>
<lattice>I</lattice>
<operator id="0">21</operator>
<operator id="1">3</operator>
<operator id="2">3</operator>
</spacegroup>
<n_symops>24</n_symops>
<symmetry_operator id="0">
<aa>1</aa> <ab>0</ab> <ac>0</ac> <atrans>0</atrans>
<ba>0</ba> <bb>1</bb> <bc>0</bc> <btrans>0</btrans>
<ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0</ctrans>
</symmetry_operator>
<symmetry_operator id="1">
<aa>-1</aa> <ab>0</ab> <ac>0</ac> <atrans>0</atrans>
<ba>0</ba> <bb>-1</bb> <bc>0</bc> <btrans>0.5</btrans>
<ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0</ctrans>
</symmetry_operator>
<symmetry_operator id="2">
<aa>1</aa> <ab>0</ab> <ac>0</ac> <atrans>0</atrans>
<ba>0</ba> <bb>-1</bb> <bc>0</bc> <btrans>0</btrans>
<ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>0.5</ctrans>
</symmetry_operator>
<symmetry_operator id="3">
<aa>-1</aa> <ab>0</ab> <ac>0</ac> <atrans>0</atrans>
<ba>0</ba> <bb>1</bb> <bc>0</bc> <btrans>0.5</btrans>
<ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>0.5</ctrans>
</symmetry_operator>
<symmetry_operator id="4">
<aa>0</aa> <ab>1</ab> <ac>0</ac> <atrans>0</atrans>
<ba>0</ba> <bb>0</bb> <bc>1</bc> <btrans>0</btrans>
<ca>1</ca> <cb>0</cb> <cc>0</cc> <ctrans>0</ctrans>
</symmetry_operator>
<symmetry_operator id="5">
<aa>0</aa> <ab>-1</ab> <ac>0</ac> <atrans>0</atrans>
<ba>0</ba> <bb>0</bb> <bc>1</bc> <btrans>0.5</btrans>
<ca>-1</ca> <cb>0</cb> <cc>0</cc> <ctrans>0</ctrans>
</symmetry_operator>
<symmetry_operator id="6">
<aa>0</aa> <ab>-1</ab> <ac>0</ac> <atrans>0</atrans>
<ba>0</ba> <bb>0</bb> <bc>-1</bc> <btrans>0</btrans>
<ca>1</ca> <cb>0</cb> <cc>0</cc> <ctrans>0.5</ctrans>
</symmetry_operator>
<symmetry_operator id="7">
<aa>0</aa> <ab>1</ab> <ac>0</ac> <atrans>0</atrans>
<ba>0</ba> <bb>0</bb> <bc>-1</bc> <btrans>0.5</btrans>
<ca>-1</ca> <cb>0</cb> <cc>0</cc> <ctrans>0.5</ctrans>
</symmetry_operator>
<symmetry_operator id="8">
<aa>0</aa> <ab>0</ab> <ac>1</ac> <atrans>0</atrans>
<ba>1</ba> <bb>0</bb> <bc>0</bc> <btrans>0</btrans>
<ca>0</ca> <cb>1</cb> <cc>0</cc> <ctrans>0</ctrans>
</symmetry_operator>
<symmetry_operator id="9">
<aa>0</aa> <ab>0</ab> <ac>-1</ac> <atrans>0</atrans>
<ba>1</ba> <bb>0</bb> <bc>0</bc> <btrans>0</btrans>
<ca>0</ca> <cb>-1</cb> <cc>0</cc> <ctrans>0.5</ctrans>
</symmetry_operator>
<symmetry_operator id="10">
<aa>0</aa> <ab>0</ab> <ac>-1</ac> <atrans>0</atrans>
<ba>-1</ba> <bb>0</bb> <bc>0</bc> <btrans>0.5</btrans>
<ca>0</ca> <cb>1</cb> <cc>0</cc> <ctrans>0.5</ctrans>
</symmetry_operator>
<symmetry_operator id="11">
<aa>0</aa> <ab>0</ab> <ac>1</ac> <atrans>0.5</atrans>
<ba>-1</ba> <bb>0</bb> <bc>0</bc> <btrans>0</btrans>
<ca>0</ca> <cb>-1</cb> <cc>0</cc> <ctrans>0.5</ctrans>
</symmetry_operator>
<symmetry_operator id="12">
<aa>1</aa> <ab>0</ab> <ac>0</ac> <atrans>0.5</atrans>
<ba>0</ba> <bb>1</bb> <bc>0</bc> <btrans>0.5</btrans>
<ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0.5</ctrans>
</symmetry_operator>
<symmetry_operator id="13">
<aa>-1</aa> <ab>0</ab> <ac>0</ac> <atrans>0.5</atrans>
<ba>0</ba> <bb>-1</bb> <bc>0</bc> <btrans>1</btrans>
<ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0.5</ctrans>
</symmetry_operator>
<symmetry_operator id="14">
<aa>1</aa> <ab>0</ab> <ac>0</ac> <atrans>0.5</atrans>
<ba>0</ba> <bb>-1</bb> <bc>0</bc> <btrans>0.5</btrans>
<ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>1</ctrans>
</symmetry_operator>
<symmetry_operator id="15">
<aa>-1</aa> <ab>0</ab> <ac>0</ac> <atrans>0.5</atrans>
<ba>0</ba> <bb>1</bb> <bc>0</bc> <btrans>1</btrans>
<ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>1</ctrans>
</symmetry_operator>
<symmetry_operator id="16">
<aa>0</aa> <ab>1</ab> <ac>0</ac> <atrans>0.5</atrans>
<ba>0</ba> <bb>0</bb> <bc>1</bc> <btrans>0.5</btrans>
<ca>1</ca> <cb>0</cb> <cc>0</cc> <ctrans>0.5</ctrans>
</symmetry_operator>
<symmetry_operator id="17">
<aa>0</aa> <ab>-1</ab> <ac>0</ac> <atrans>0.5</atrans>
<ba>0</ba> <bb>0</bb> <bc>1</bc> <btrans>1</btrans>
<ca>-1</ca> <cb>0</cb> <cc>0</cc> <ctrans>0.5</ctrans>
</symmetry_operator>
<symmetry_operator id="18">
<aa>0</aa> <ab>-1</ab> <ac>0</ac> <atrans>0.5</atrans>
<ba>0</ba> <bb>0</bb> <bc>-1</bc> <btrans>0.5</btrans>
<ca>1</ca> <cb>0</cb> <cc>0</cc> <ctrans>1</ctrans>
</symmetry_operator>
<symmetry_operator id="19">
<aa>0</aa> <ab>1</ab> <ac>0</ac> <atrans>0.5</atrans>
<ba>0</ba> <bb>0</bb> <bc>-1</bc> <btrans>1</btrans>
<ca>-1</ca> <cb>0</cb> <cc>0</cc> <ctrans>1</ctrans>
</symmetry_operator>
<symmetry_operator id="20">
<aa>0</aa> <ab>0</ab> <ac>1</ac> <atrans>0.5</atrans>
<ba>1</ba> <bb>0</bb> <bc>0</bc> <btrans>0.5</btrans>
<ca>0</ca> <cb>1</cb> <cc>0</cc> <ctrans>0.5</ctrans>
</symmetry_operator>
<symmetry_operator id="21">
<aa>0</aa> <ab>0</ab> <ac>-1</ac> <atrans>0.5</atrans>
<ba>1</ba> <bb>0</bb> <bc>0</bc> <btrans>0.5</btrans>
<ca>0</ca> <cb>-1</cb> <cc>0</cc> <ctrans>1</ctrans>
</symmetry_operator>
<symmetry_operator id="22">
<aa>0</aa> <ab>0</ab> <ac>-1</ac> <atrans>0.5</atrans>
<ba>-1</ba> <bb>0</bb> <bc>0</bc> <btrans>1</btrans>
<ca>0</ca> <cb>1</cb> <cc>0</cc> <ctrans>1</ctrans>
</symmetry_operator>
<symmetry_operator id="23">
<aa>0</aa> <ab>0</ab> <ac>1</ac> <atrans>1</atrans>
<ba>-1</ba> <bb>0</bb> <bc>0</bc> <btrans>0.5</btrans>
<ca>0</ca> <cb>-1</cb> <cc>0</cc> <ctrans>1</ctrans>
</symmetry_operator>
</dataset_info>
<solution_info>
<file type="XYZ" format="PDB">insulin.pdb</file>
<file type="HKL" format="MTZ">insulin.mtz</file>
<llg>81640.054723</llg>
</solution_info>
</phaser>
</pre>

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		+	[[Category:Phaser-2.2]]
	Phaser can generate XML output from keyword input. XML output should be used in preference to grepping logfiles when incorporating Phaser into automation pipelines. Note that Phaser's python scripting ability is a more powerful way of calling Phaser for automation pipelines.		Phaser can generate XML output from keyword input. XML output should be used in preference to grepping logfiles when incorporating Phaser into automation pipelines. Note that Phaser's python scripting ability is a more powerful way of calling Phaser for automation pipelines.

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 <div style="margin-left: 25px; float: right;">__TOC__</div>
-[[Category:Phaser-2.2]]
 Phaser can generate XML output from keyword input. XML output should be used in preference to grepping logfiles when incorporating Phaser into automation pipelines. Note that Phaser's python scripting ability is a more powerful way of calling Phaser for automation pipelines.

← Older revision	Revision as of 13:02, 7 September 2009
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← Older revision	Revision as of 09:33, 9 July 2009
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XML - Revision history

WikiSysop at 15:55, 7 September 2009

WikiSysop: category

WikiSysop: moved Phaser-2.2: XML to XML: take of phaser-2.2 page header so that it can be reused

WikiSysop: Protected "Phaser-2.2: XML" ([edit=sysop] (indefinite) [move=sysop] (indefinite))

WikiSysop: Initialization from almanac